|
| Status |
Public on Apr 07, 2021 |
| Title |
NMYC_RB_3056 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse tumor
|
| Organism |
Mus musculus |
| Characteristics |
age: 8 weeks
genotype: Pb-Cre+; Pten f/f; Rb1 f/f; MYCN+
status: Intact
tissue: prostate tumors
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Prostate tumors were digested using 1 mg/mL collagenase and 0.2 mg/mL hyaluronidase for 1 hour at 37C followed by additional digestion with TrypLE for 15 minutes at 37C. Digestions were inactivated with media containing 1x B-27 supplement.
Libraries were generated using the 10x Genomics Chromium Single Cell ATAC Library Kit following the manufacturer's recommended protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
scATAC-seq reads were aligned to mm10 reference genome using the cellranger-atac count pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered HDF5 feature barcode and transcription factor matrix files generated using the cellranger-atac count pipeline.
|
| |
|
| Submission date |
May 29, 2020 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Nicholas Brady |
| E-mail(s) |
njb2003@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
1188 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE151425 |
Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [scATAC-seq] |
| GSE151426 |
Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer |
|
| Relations |
| BioSample |
SAMN15053670 |
| SRA |
SRX8423455 |
